Aiming at Chinese high IPO underpricing rate phenomenon in domestic capital market, we selected 214 private equity backed enterprises during 2009—2015 as sample to study this topic which are listed in small and medium enterprise board, this paper discusses the influence of equity structure and intermediary agency reputation on IPO underpricing rate. The empirical results show that there is a significant “invertedU” type of nonlinear relationship between the first shareholder’s shareholding ratio and IPO underpricing rate, and that there is a negative relation between the leading underwriter’s reputation and underpricing rate. However, there are no significant relations among the reputation of accounting firms and law firms, the shareholding ratio of the second to the tenth shareholders, first PE agency reputation and shareholding rate, the shareholding rate of board of directors and executives, the proportion of circulation stock and IPO underpricing rate.